[Bioc-devel] Samtools dependency

Pages, Herve hp@ge@ @end|ng |rom |redhutch@org
Fri Aug 23 20:22:42 CEST 2019

Hi Jonathon,

Have you considered depending on Rhtslib? See 

Rsamtools itself is implemented on top of Rhtslib. Note that other 
Bioconductor packages (e.g. DiffBind, deepSNV, BitSeq, qrqc, QuasR, 
seqbias, TransView, etc...) use Rhtslib internally to implement features 
not implemented in Rsamtools.


On 8/23/19 11:05, Jonathon Hill wrote:
> Hi,
> I am working through the process of submitting a new package (MMAPPR2). We are having a problem with the build failing, because our package requires Samtools installed. We cannot use Rsamtools, as we depend on features not implemented in the package. How do we resolve the issue? What is the policy for system dependencies? We have samtools listed in the DESCRIPTION and installation instructions in our README, but I am sure that is not enough to get it installed on the Build and Check servers.
> Thanks,
> Jonathon Hill
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Hervé Pagès

Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
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